Cylinder definition changes legacy .stinput files

[nicholasbl]

Describe the bug
Cylinders, as of 0865001 , are now defined by their centers. This, however, breaks legacy .stinput files.

Expected behavior
.stinput files should either:

• load with a tweak (rotation * radius offset) for cylinder geometries
• emit a warning/rejection letting folks know to update their input files

[jmaack24]

Unless we want to start versioning the stinput files (I don't think we should do that...), we should probably use the offset fix.

The correction can be found in this test TEST(NativeRunner, ValidationTest2) in the native_runner_validation_test.cpp file. I fixed it for this test and for some reason didn't think about this being an issue for other stinput files...